uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ControlledVocabularyRepository java code examples

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}

public static void check( ) {
  initialise( );
}

        if ( ControlledVocabularyRepository.getIdentityQualifier().equals( xref.getCvXrefQualifier() ) )
                    ControlledVocabularyRepository.getNoUniprotUpdateTopic() );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
proteinType.addAnnotation( annotation );

 bibRef.getSecondary(),
 bibRef.getVersion(),
 ControlledVocabularyRepository.getPrimaryXrefQualifier() );
xrefTag.getSecondary(),
xrefTag.getVersion(),
ControlledVocabularyRepository.getSeeAlsoXrefQualifier() );

Xref xref = (Xref) iterator.next();
if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) {
  if ( ControlledVocabularyRepository.getPrimaryXrefQualifier().equals( xref.getCvXrefQualifier() ) ) {

CvXrefQualifier identity = ControlledVocabularyRepository.getIdentityQualifier();

CvAliasType geneNameAliasType = ControlledVocabularyRepository.getGeneNameAliasType();
if ( geneNameAliasType != null ) {
  for ( Iterator iterator = protein.getAliases().iterator(); iterator.hasNext() && geneName == null; ) {

if ( confidence != null ) {
  final CvTopic authorConfidence = ControlledVocabularyRepository.getAuthorConfidenceTopic();

ControlledVocabularyRepository.check( );

        if ( ControlledVocabularyRepository.getIdentityQualifier().equals( xref.getCvXrefQualifier() ) )
                    ControlledVocabularyRepository.getNoUniprotUpdateTopic() );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
proteinType.addAnnotation( annotation );

 bibRef.getSecondary(),
 bibRef.getVersion(),
 ControlledVocabularyRepository.getPrimaryXrefQualifier() );
xrefTag.getSecondary(),
xrefTag.getVersion(),
ControlledVocabularyRepository.getSeeAlsoXrefQualifier() );

Xref xref = (Xref) iterator.next();
if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) {
  if ( ControlledVocabularyRepository.getPrimaryXrefQualifier().equals( xref.getCvXrefQualifier() ) ) {

private static void createXref( Protein protein,
                XrefTag xrefTag,
                boolean identity ) throws IntactException {
  CvXrefQualifier qualifier = null;
  if ( identity ) {
    qualifier = ControlledVocabularyRepository.getIdentityQualifier();
  }
  CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() );
  if ( database == null ) {
    // failed to find the database, skip the Xref creation
  } else {
    InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(),
               database,
               xrefTag.getId(),
               xrefTag.getSecondary(),
               xrefTag.getVersion(),
               qualifier );
    protein.addXref( xref );
    IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
  }
}

CvAliasType geneNameAliasType = ControlledVocabularyRepository.getGeneNameAliasType();
if ( geneNameAliasType != null ) {
  for ( Iterator iterator = protein.getAliases().iterator(); iterator.hasNext() && geneName == null; ) {

if ( confidence != null ) {
  final CvTopic authorConfidence = ControlledVocabularyRepository.getAuthorConfidenceTopic();

ControlledVocabularyRepository.check( );

        if ( ControlledVocabularyRepository.getIdentityQualifier().equals( xref.getCvXrefQualifier() ) )
                    ControlledVocabularyRepository.getNoUniprotUpdateTopic() );
IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getAnnotationDao().persist( annotation );
proteinType.addAnnotation( annotation );

 bibRef.getSecondary(),
 bibRef.getVersion(),
 ControlledVocabularyRepository.getPrimaryXrefQualifier() );
xrefTag.getSecondary(),
xrefTag.getVersion(),
ControlledVocabularyRepository.getSeeAlsoXrefQualifier() );

Xref xref = (Xref) iterator.next();
if ( CvDatabase.PSI_MI.equals( xref.getCvDatabase().getShortLabel() ) ) {
  if ( ControlledVocabularyRepository.getPrimaryXrefQualifier().equals( xref.getCvXrefQualifier() ) ) {

private static void createXref( Protein protein,
                XrefTag xrefTag,
                boolean identity ) throws IntactException {
  CvXrefQualifier qualifier = null;
  if ( identity ) {
    qualifier = ControlledVocabularyRepository.getIdentityQualifier();
  }
  CvDatabase database = XrefChecker.getCvDatabase( xrefTag.getDb() );
  if ( database == null ) {
    // failed to find the database, skip the Xref creation
  } else {
    InteractorXref xref = new InteractorXref( IntactContext.getCurrentInstance().getInstitution(),
               database,
               xrefTag.getId(),
               xrefTag.getSecondary(),
               xrefTag.getVersion(),
               qualifier );
    protein.addXref( xref );
    IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getXrefDao().persist( xref );
  }
}

public static void check( ) {
  initialise( );
}

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How to useControlledVocabularyRepository in uk.ac.ebi.intact.application.dataConversion.psiUpload.checker

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ControlledVocabularyRepository (Showing top 20 results out of 315)

How to use
ControlledVocabularyRepository
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uk.ac.ebi.intact.application.dataConversion.psiUpload.checker